5,051 research outputs found
Application of Markov Stability for graph-based clustering on protein-protein interaction networks
Protein-Protein interaction networks are one of the most well-explored and documented parts of the interactome, as such, they have had a variety of databases and analyses developed for them, in order to harness this highly useful abstraction of very complex systems. Community detection is a popular analysis for many datasets which can be abstracted onto graphs and otherwise is a concept still performed on non-graph-based datasets through clustering methods. Community detection can also be performed at varying scales through the introduction of artificial time parameters, which in this case is a result of the use of a measure called Markov Stability. Markov Stability is also used as a measure to define a good graph partition but optimizing by having it be the objective function of the Louvain algorithm. In this study, we implement a framework for multiscale community detection governed by Markov stability, which has been previously used in other studies and apply this framework to an example protein-protein network of the proteins related to the 20 most frequently mutated human cancer genes from the STRING database. The results of this application are then explored and we show that due to the underlying properties of the example, robust partitions are obtained across varying Markov times
“Oh my god, how did I spend all that money?”: Lived experiences in two commodified fandom communities
This research explores the role of commodification in participation in celebrity-centric fandom communities, applying a leisure studies framework to understand the constraints fans face in their quest to participate and the negotiations they engage in to overcome these constraints.
In fan studies scholarship, there is a propensity to focus on the ways fans oppose commodified industry structures; however, this ignores the many fans who happily participate within them. Using the fandoms for the pop star Taylor Swift and the television series Supernatural as case studies, this project uses a mixed-methodological approach to speak directly to fans via surveys and semistructured interviews to develop an understanding of fans’ lived experiences based on their own words.
By focusing on celebrity-centric fandom communities rather than on the more frequently studied textual fandoms, this thesis turns to the role of the celebrity in fans’ ongoing desire to participate in commodified spaces. I argue that fans are motivated to continue spending money to participate within their chosen fandom when this form of participation is tied to the opportunity for engagement with the celebrity. While many fans seek community from their fandom participation, this research finds that for others, social ties are a secondary outcome of their overall desire for celebrity attention, which becomes a hobby in which they build a “leisure career” (Stebbins 2014). When fans successfully gain attention from their celebrity object of fandom, they gain status within their community, creating intra-fandom hierarchies based largely on financial resources and on freedom from structural constraints related to education, employment, and caring.
Ultimately, this thesis argues that the broad neglect of celebrity fandom practices means we have overlooked the experiences of many fans, necessitating a much broader future scope for the field
Operatic Pasticcios in 18th-Century Europe
In Early Modern times, techniques of assembling, compiling and arranging pre-existing material were part of the established working methods in many arts. In the world of 18th-century opera, such practices ensured that operas could become a commercial success because the substitution or compilation of arias fitting the singer's abilities proved the best recipe for fulfilling the expectations of audiences. Known as »pasticcios« since the 18th-century, these operas have long been considered inferior patchwork. The volume collects essays that reconsider the pasticcio, contextualize it, define its preconditions, look at its material aspects and uncover its aesthetical principles
Line game-perfect graphs
The -edge colouring game is played with a set of colours on a
graph with initially uncoloured edges by two players, Alice (A) and Bob
(B). The players move alternately. Player has the first move.
. If , then only player may skip any move,
otherwise skipping is not allowed for any player. A move consists in colouring
an uncoloured edge with one of the colours such that adjacent edges have
distinct colours. When no more moves are possible, the game ends. If every edge
is coloured in the end, Alice wins; otherwise, Bob wins.
The -game chromatic index is the smallest
nonnegative integer such that Alice has a winning strategy for the
-edge colouring game played on with colours. The graph is
called line -perfect if, for any edge-induced subgraph of ,
where denotes the clique
number of the line graph of .
For each of the six possibilities , we
characterise line -perfect graphs by forbidden (edge-induced) subgraphs
and by explicit structural descriptions, respectively
Partitioning algorithms for induced subgraph problems
This dissertation introduces the MCSPLIT family of algorithms for two closely-related NP-hard problems that involve finding a large induced subgraph contained by each of two input graphs: the induced subgraph isomorphism problem and the maximum common induced subgraph problem.
The MCSPLIT algorithms resemble forward-checking constrant programming algorithms, but use problem-specific data structures that allow multiple, identical domains to be stored without duplication. These data structures enable fast, simple constraint propagation algorithms and very fast calculation of upper bounds. Versions of these algorithms for both sparse and dense graphs are described and implemented. The resulting algorithms are over an order of magnitude faster than the best existing algorithm for maximum common induced subgraph on unlabelled graphs, and outperform the state of the art on several classes of induced subgraph isomorphism instances.
A further advantage of the MCSPLIT data structures is that variables and values are treated identically; this allows us to choose to branch on variables representing vertices of either input graph with no overhead. An extensive set of experiments shows that such two-sided branching can be particularly beneficial if the two input graphs have very different orders or densities. Finally, we turn from subgraphs to supergraphs, tackling the problem of finding a small graph that contains every member of a given family of graphs as an induced subgraph. Exact and heuristic techniques are developed for this problem, in each case using a MCSPLIT algorithm as a subroutine. These algorithms allow us to add new terms to two entries of the On-Line Encyclopedia of Integer Sequences
Determinantal Sieving
We introduce determinantal sieving, a new, remarkably powerful tool in the
toolbox of algebraic FPT algorithms. Given a polynomial on a set of
variables and a linear matroid of
rank , both over a field of characteristic 2, in
evaluations we can sieve for those terms in the monomial expansion of which
are multilinear and whose support is a basis for . Alternatively, using
evaluations of we can sieve for those monomials whose odd support
spans . Applying this framework, we improve on a range of algebraic FPT
algorithms, such as:
1. Solving -Matroid Intersection in time and -Matroid
Parity in time , improving on (Brand and Pratt,
ICALP 2021)
2. -Cycle, Colourful -Path, Colourful -Linkage in undirected
graphs, and the more general Rank -Linkage problem, all in
time, improving on respectively (Fomin et al., SODA 2023)
3. Many instances of the Diverse X paradigm, finding a collection of
solutions to a problem with a minimum mutual distance of in time
, improving solutions for -Distinct Branchings from time
to (Bang-Jensen et al., ESA 2021), and for Diverse
Perfect Matchings from to (Fomin et al.,
STACS 2021)
All matroids are assumed to be represented over a field of characteristic 2.
Over general fields, we achieve similar results at the cost of using
exponential space by working over the exterior algebra. For a class of
arithmetic circuits we call strongly monotone, this is even achieved without
any loss of running time. However, the odd support sieving result appears to be
specific to working over characteristic 2
Stake-governed tug-of-war and the biased infinity Laplacian
In tug-of-war, two players compete by moving a counter along edges of a
graph, each winning the right to move at a given turn according to the flip of
a possibly biased coin. The game ends when the counter reaches the boundary, a
fixed subset of the vertices, at which point one player pays the other an
amount determined by the boundary vertex. Economists and mathematicians have
independently studied tug-of-war for many years, focussing respectively on
resource-allocation forms of the game, in which players iteratively spend
precious budgets in an effort to influence the bias of the coins that determine
the turn victors; and on PDE arising in fine mesh limits of the constant-bias
game in a Euclidean setting.
In this article, we offer a mathematical treatment of a class of tug-of-war
games with allocated budgets: each player is initially given a fixed budget
which she draws on throughout the game to offer a stake at the start of each
turn, and her probability of winning the turn is the ratio of her stake and the
sum of the two stakes. We consider the game played on a tree, with boundary
being the set of leaves, and the payment function being the indicator of a
single distinguished leaf. We find the game value and the essentially unique
Nash equilibrium of a leisurely version of the game, in which the move at any
given turn is cancelled with constant probability after stakes have been
placed. We show that the ratio of the players' remaining budgets is maintained
at its initial value ; game value is a biased infinity harmonic
function; and the proportion of remaining budget that players stake at a given
turn is given in terms of the spatial gradient and the -derivative of
game value. We also indicate examples in which the solution takes a different
form in the non-leisurely game.Comment: 69 pages with four figures. Updated to include discussion of the
economics literature of tug-of-wa
Mars delivery service - development of the electro-mechanical systems of the Sample Fetch Rover for the Mars Sample Return Campaign
This thesis describes the development of the Sample Fetch Rover (SFR), studied for Mars Sample Return (MSR), an international campaign carried out in cooperation between the National Aeronautics and Space Administration (NASA) and the European Space Agency (ESA). The focus of this document is the design of the electro-mechanical systems of the rover.
After placing this work into the general context of robotic planetary exploration and summarising the state of the art for what concerns Mars rovers, the architecture of the Mars Sample Return Campaign is presented. A complete overview of the current SFR architecture is provided, touching upon all the main subsystems of the spacecraft. For each area, it is discussed what are the design drivers, the chosen solutions and whether they use heritage technology (in particular from the ExoMars Rover) or new developments. This research focuses on two topics of particular interest, due to their relevance for the mission and the novelty of their design: locomotion and sample acquisition, which are discussed in depth.
The early SFR locomotion concepts are summarised, covering the initial trade-offs and discarded designs for higher traverse performance. Once a consolidated architecture was reached, the locomotion subsystem was developed further, defining the details of the suspension, actuators, deployment mechanisms and wheels. This technology is presented here in detail, including some key analysis and test results that support the design and demonstrate how it responds to the mission requirements.
Another major electro-mechanical system developed as part of this work is the one dedicated to sample tube acquisition. The concept of operations of this machinery was defined to be robust against the unknown conditions that characterise the mission. The design process led to a highly automated robotic system which is described here in its main components: vision system, robotic arm and tube storage
Identification of Micro- and Submicron (Nano) Plastics in Water Sources and the Impact of COVID-19 on Plastic Pollution
One of the most significant environmental issues that our society may deal with this century could be plastics. The world's water bodies, as well as land and air, are becoming more and more contaminated by plastic due to the ongoing and expanding manufacturing of these synthetic materials, as well as the lack of an effective strategy for managing plastic waste. The fact that plastics break down into smaller particles (micro and nanoplastics) by action of environmental physical and chemical reactions, and do not degrade biologically in a reasonable time, is a cause of concern as plastics are believed to cause harm in animals, plants and humans.To identify the types of plastics prevalent in aquatic habitats, a number of procedures have been developed, from sampling to identification. After a water body has been sampled using nets, pumps, or other tools, depending on the type of sample taken, it is usually necessary to treat the samples for separation and purification. The next stage is to employ analytical techniques to identify the synthetic contaminants. The most common approaches are microscopy, spectroscopy, and thermal analysis. This thesis gives an overview of where in the environment microplastics (MPs) and nanoplastics (NPs) can be found and summarizes the most important technologies applied to analyse the importance of plastics as a contaminant in water bodies. The development of standardised analytical procedures is still necessary as most of them are not suitable for the identification of particles below 50 μm due to resolution limitations. The preparation and analysis of samples are usually time-consuming factors that shall be considered. Particularly for MP and NP analysis in aqueous samples, thermal analysis methods based on sample degradation are generally not considered to be the most effective approach. Nevertheless, Pyrolysis - Gas Chromatography Time-of-Flight Mass Spectrometry (Py-GCToFMS) is used in this thesis to propose a novel approach as due to its unique detection abilities, and with a novel filtration methodology for collection, it enables the identification of tiny particle sizes (>0.1 μm) in water samples.PTFE membranes were selected to filter the liquid samples using a glass filtration system. This way, the synthetic particles will be deposited on the membranes and will allow the study and analysis of the precipitated material. PTFE is a readily available, reasonably priced, and adaptable product that makes sample preparation quick and simple.The three plastics under study—polypropylene (PP), polystyrene (PS), and polyvinyl chloride (PVC)—can be identified from complex samples at trace levels thanks to the employment of these widely used membranes and the identification of various and specific (marker) ions. The technique was examined against a range of standards samples that contained predetermined concentrations of MPs and NPs. Detection levels were then determined for PVC and PS and were found to be below <50 μg/ L, with repeatable data showing good precision (RSD <20 %). The examination of a complex matrix sample taken from a nearby river contributed to further validate this innovative methodology; the results indicated the existence of PS with a semi-quantifiable result of 250.23 g/L. Because of this, PY-GCToFMS appears to be a method that is appropriate for the task of identifying MPs and NPs from complex mixtures.This thesis also focuses on the environmental challenge that disposable plastic face masks (DPFMs) pose, which has been made significantly worse due to the COVID-19 pandemic. By the time this thesis was written, the production of disposable plastic facemasks had reached to approximately 200 million a day, in a global effort to tackle the spread of the new SARS-CoV-2 virus. This thesis investigates the emissions of pollutants from several different DPFM brands (medical and non-medical) that were submerged in water to replicate the conditions in the environment after these DPFMs have been discarded. The DPFM leachates were filtered using inorganic membranes type and characterized using Fourier transform infrared spectroscopy (FTIR), Scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDS), Light/Optical Microscopy (LM/OM), Inductively coupled plasma mass spectrometry (ICP-MS) and Liquid chromatography–mass spectrometry (LC-MS). Micro and nano scale polymeric fibres, particles, siliceous fragments and leachable inorganic and organic chemicals were observed from all of the tested DPFMs. For non-medical DPFMs, traces of concerning heavy metals were detected in association with silicon containing fragments (i.e. lead up to 6.79 μg/L). ICP-MS also confirmed the presence of other leachable metals like cadmium (up to 1.92 μg/L), antimony (up to 3.93 μg/L) and copper (up to 4.17 μg/L). LC-MS analysis identified organic species related to plastic additives; polyamide-66 monomer and oligomers (nylon-66 synthesis), surfactant molecules, and dye-like molecules were all tentatively identified in the leachate. The question of whether DPFMs are safe to use daily and what implications may be anticipated after their disposal into the environment is brought up by the toxicity of some of the chemicals discovered.The previous approach is expanded to medical DPFMs with the utilisation of Field Emission Gun Scanning Electron Microscope (FEG-SEM) in order to get high resolution images of the micro and nanoparticles deposited on the membranes. It is also incorporated the use of 0.02 μm pore size inorganic membranes to better identify the nanoparticles released.Separated aqueous samples were also obtained by submerging medical DPFMs for 24 hours to be analysed using ICP-MS and LC-MS.Both particles and fibres in the micro and nano scale were found in all 6 DPFMs brands of this study. EDS analysis revealed the presence of particles containing different heavy metals like lead, mercury, and arsenic among others. ICP-MS analysis results confirmed traces of heavy metals (antimony up to 2.41 μg/L and copper up to 4.68 μg/L). LC-MS analysis results identified organic species related to plastic additives and contaminants; polyamide-66 monomer and oligomers (nylon-66 synthesis), surfactant molecules, and polyethylene glycol were all tentatively identified in the leachate. The toxicity of some of the chemicals found raises the question of whether DPFMs are safe to be used on a daily basis and what consequences are to be expected after their disposal into the environment
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